SARS-CoV-2 Lineage Variant Summary


Nucleotide variants related to lineages of concern and observed in > 20% of sequences are indicated in yellow above a schematic SARS-CoV-2 genome. Primers that do not overlap with variants associated with these lineages at are shown in green. Primers that do overlap are indicated in orange.

Overlapping amplicons:


Orf1 Gene (1.5 kb) Variants


Orf1 Gene (10 kb) Variants


Orf1 Gene (14 kb) Variants


Orf1 Gene (19 kb) Variants


S Gene Variants


Orf3a-Orf7a Gene Variants


N Gene Variants


Methods:

Sequences reported in Sequence Sources for each lineage were aligned to the NC_045512.2 reference sequence (minimap2). Variants > 20% frequency (freebayes) were evaluated for overlap with primer regions (bedtools) and displayed (Geneious Prime 2021.0.3).


Sequence Sources:

B.1.117: Virological. “Preliminary Genomic Characterisation of an Emergent SARS-CoV-2 Lineage in the UK Defined by a Novel Set of Spike Mutations - SARS-CoV-2 Coronavirus / NCoV-2019 Genomic Epidemiology,” December 18, 2020. https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 .

B.1.351: Tegally, Houriiyah, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, et al. “Emergence and Rapid Spread of a New Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2) Lineage with Multiple Spike Mutations in South Africa.” MedRxiv, December 22, 2020, 2020.12.21.20248640. https://doi.org/10.1101/2020.12.21.20248640 .

P.1: Virological. “SARS-CoV-2 Reinfection by the New Variant of Concern (VOC) P.1 in Amazonas, Brazil - SARS-CoV-2 Coronavirus / NCoV-2019 Genomic Epidemiology,” January 18, 2021. https://virological.org/t/sars-cov-2-reinfection-by-the-new-variant-of-concern-voc-p-1-in-amazonas-brazil/596 .

B.1.526: West, Anthony P., Joel O. Wertheim, Jade C. Wang, Tetyana I. Vasylyeva, Jennifer L. Havens, Moinuddin A. Chowdhury, Edimarlyn Gonzalez, et al. “Detection and Characterization of the SARS-CoV-2 Lineage B.1.526 in New York.” BioRxiv, April 22, 2021, 2021.02.14.431043. https://doi.org/10.1101/2021.02.14.431043.

B.1.617.1: GitHub. “Possible New Emerging Sub-Lineage under Recently Designated Lineage B.1.617 · Issue #55 · Cov-Lineages/Pango-Designation.” Accessed June 20, 2021. https://github.com/cov-lineages/pango-designation/issues/55.

B.1.617.2: GitHub. “Potential Sequences That Should Be Included in B.1.617 · Issue #49 · Cov-Lineages/Pango-Designation.” Accessed June 20, 2021. https://github.com/cov-lineages/pango-designation/issues/49.

AY.1: GitHub. “B.1.617.2 Sublineage with K417N · Issue #95 · Cov-Lineages/Pango-Designation.” Accessed June 20, 2021. https://github.com/cov-lineages/pango-designation/issues/95.

C.37: GitHub. “Subclade of B.1.1.1 (Resulting from a Discrete Evolutionary Sprint in December/January?) Widespread in Chile · Issue #52 · Cov-Lineages/Pango-Designation.” Accessed June 21, 2021. https://github.com/cov-lineages/pango-designation/issues/52.


Amplicon Designs:

US CDC: Lu, Xiaoyan, Lijuan Wang, Senthilkumar K. Sakthivel, Brett Whitaker, Janna Murray, Shifaq Kamili, Brian Lynch, et al. “US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 - Volume 26, Number 8—August 2020 - Emerging Infectious Diseases Journal - CDC.” Accessed April 23, 2021. https://doi.org/10.3201/eid2608.201246.

China CDC: “新型冠状病毒核酸检测引物和探针序列(Specific Primers and Probes for Detection 2019 Novel Coronavirus).” Accessed June 20, 2021. http://ivdc.chinacdc.cn/kyjz/202001/t20200121_211337.html.

Charité: Corman, Victor M., Olfert Landt, Marco Kaiser, Richard Molenkamp, Adam Meijer, Daniel KW Chu, Tobias Bleicker, et al. “Detection of 2019 Novel Coronavirus (2019-NCoV) by Real-Time RT-PCR.” Eurosurveillance 25, no. 3 (January 23, 2020): 2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045a.

ARTIC v3: Tyson, John R., Phillip James, David Stoddart, Natalie Sparks, Arthur Wickenhagen, Grant Hall, Ji Hyun Choi, et al. “Improvements to the ARTIC Multiplex PCR Method for SARS-CoV-2 Genome Sequencing Using Nanopore.” BioRxiv: The Preprint Server for Biology, September 4, 2020. https://doi.org/10.1101/2020.09.04.283077.

Midnight 1200 bp: Freed, Nikki E., Markéta Vlková, Muhammad B. Faisal, and Olin K. Silander. “Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 Using 1200 Bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding.” Biology Methods & Protocols 5, no. 1 (2020): bpaa014. https://doi.org/10.1093/biomethods/bpaa014.

ARTIC v4: ARTIC Real-time Genomic Surveillance. “SARS-CoV-2 Version 4 Scheme Release - Laboratory,” June 24, 2021. https://community.artic.network/t/sars-cov-2-version-4-scheme-release/312.


Software Tools:

Li, Heng. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34, no. 18 (September 15, 2018): 3094–3100. https://doi.org/10.1093/bioinformatics/bty191 .

Garrison, Erik, and Gabor Marth. “Haplotype-Based Variant Detection from Short-Read Sequencing.” ArXiv:1207.3907 [q-Bio], July 20, 2012. http://arxiv.org/abs/1207.3907.

Quinlan, Aaron R, and Ira M Hall. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics (Oxford, England) 26 (2010): 841–42. https://doi.org/10.1093/bioinformatics/btq033 .

Geneious version 2021.1 created by Biomatters. Available from https://www.geneious.com


History:

2021-06-20: Updated to currently relevant variants of concerns.

2021-06-24: Added ARTICv4